Calcium in PDB 3t8d: Thermolysin in Complex with UBTLN31

All present enzymatic activity of Thermolysin in Complex with UBTLN31:
3.4.24.27;

The structure of Thermolysin in Complex with UBTLN31, PDB code: 3t8d was solved by A.Biela, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.68 / 1.41
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.800, 92.800, 130.100, 90.00, 90.00, 120.00
R / Rfree (%)	12.6 / 15.3

The structure of Thermolysin in Complex with UBTLN31 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin in Complex with UBTLN31 (pdb code 3t8d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Thermolysin in Complex with UBTLN31, PDB code: 3t8d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin in Complex with UBTLN31


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin in Complex with UBTLN31 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca326 b:10.7 occ:1.00 O A:ASN183 2.3 12.0 1.0 O A:HOH487 2.3 12.8 1.0 OE2 A:GLU190 2.3 9.6 1.0 O A:HOH500 2.4 11.8 1.0 OD2 A:ASP185 2.4 11.4 1.0 OE2 A:GLU177 2.4 9.5 1.0 CG A:ASP185 3.2 10.3 1.0 CD A:GLU177 3.2 8.6 1.0 CD A:GLU190 3.3 9.0 1.0 C A:ASN183 3.5 12.3 1.0 OD1 A:ASP185 3.6 9.7 1.0 OE1 A:GLU177 3.8 8.8 1.0 CA A:CA327 3.8 8.8 1.0 CG A:GLU190 3.8 9.6 1.0 CB A:ASN183 4.1 16.8 1.0 CA A:PRO184 4.1 11.0 1.0 N A:ASP185 4.2 9.6 1.0 OD2 A:ASP191 4.2 13.7 1.0 O A:HOH692 4.2 34.7 1.0 CG A:GLU177 4.2 8.8 1.0 C A:PRO184 4.2 11.2 1.0 OD1 A:ASP191 4.3 12.9 1.0 OE1 A:GLU190 4.3 9.3 1.0 N A:PRO184 4.3 11.5 1.0 CB A:ASP185 4.4 9.1 1.0 O A:LYS182 4.4 15.0 1.0 CA A:ASN183 4.5 14.4 1.0 O A:HOH641 4.5 23.0 1.0 CG A:ASP191 4.5 12.1 1.0 CA A:ASP185 4.9 9.2 1.0 O A:PRO184 4.9 12.6 1.0

Calcium binding site 2 out of 4 in the Thermolysin in Complex with UBTLN31


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin in Complex with UBTLN31 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca327 b:8.8 occ:1.00 O A:GLU187 2.3 9.2 1.0 OD2 A:ASP138 2.4 8.1 1.0 O A:HOH378 2.4 8.6 1.0 OE1 A:GLU177 2.5 8.8 1.0 OD1 A:ASP185 2.5 9.7 1.0 OE1 A:GLU190 2.5 9.3 1.0 OE2 A:GLU190 2.5 9.6 1.0 OE2 A:GLU177 2.7 9.5 1.0 CD A:GLU190 2.8 9.0 1.0 CD A:GLU177 2.9 8.6 1.0 CG A:ASP138 3.4 8.0 1.0 C A:GLU187 3.4 9.3 1.0 CG A:ASP185 3.5 10.3 1.0 CA A:CA326 3.8 10.7 1.0 OD2 A:ASP185 3.9 11.4 1.0 CB A:ASP138 4.0 7.6 1.0 O A:ASP185 4.2 9.5 1.0 N A:GLU187 4.2 9.7 1.0 N A:ILE188 4.3 9.2 1.0 OD1 A:ASP138 4.3 10.5 1.0 CA A:GLU187 4.3 10.2 1.0 O A:HOH641 4.3 23.0 1.0 CA A:ILE188 4.3 9.1 1.0 CG A:GLU190 4.3 9.6 1.0 CG A:GLU177 4.4 8.8 1.0 N A:GLY189 4.4 8.2 1.0 O A:HOH510 4.5 15.0 1.0 CB A:GLU187 4.6 12.2 1.0 C A:ASP185 4.6 9.6 1.0 C A:ILE188 4.8 8.6 1.0 CB A:ASP185 4.8 9.1 1.0 N A:ASP185 4.8 9.6 1.0 CB A:GLU177 4.9 8.1 1.0 O A:HOH500 4.9 11.8 1.0 N A:GLU190 5.0 9.3 1.0

Calcium binding site 3 out of 4 in the Thermolysin in Complex with UBTLN31


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin in Complex with UBTLN31 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca328 b:12.6 occ:1.00 O A:ILE197 2.3 15.4 1.0 O A:TYR193 2.3 12.4 1.0 OD1 A:ASP200 2.4 13.4 1.0 O A:THR194 2.4 12.8 1.0 OG1 A:THR194 2.4 12.3 1.0 O A:HOH534 2.4 16.6 1.0 O A:HOH490 2.4 13.0 1.0 C A:THR194 3.2 12.3 1.0 C A:TYR193 3.3 10.6 1.0 CB A:THR194 3.4 12.1 1.0 CG A:ASP200 3.5 13.2 1.0 C A:ILE197 3.5 17.3 1.0 CA A:THR194 3.6 11.2 1.0 OD2 A:ASP200 3.8 14.2 1.0 N A:THR194 3.9 10.6 1.0 CA A:ILE197 4.2 18.8 1.0 N A:PRO195 4.3 14.4 1.0 CB A:ILE197 4.3 19.7 1.0 N A:ILE197 4.3 19.3 1.0 O A:HOH344 4.4 32.1 1.0 O A:ASP200 4.5 13.2 1.0 N A:SER198 4.5 18.6 1.0 CA A:TYR193 4.5 11.1 1.0 O A:GLU190 4.6 10.6 1.0 O A:HOH644 4.6 24.7 1.0 CA A:SER198 4.7 21.2 1.0 N A:ASP200 4.7 14.3 1.0 CD2 A:TYR193 4.7 14.3 1.0 CB A:TYR193 4.7 12.4 1.0 CA A:PRO195 4.7 16.2 1.0 CG2 A:THR194 4.8 12.4 1.0 CB A:ASP200 4.8 12.8 1.0 C A:ASP200 4.8 13.0 1.0 O A:HOH728 4.9 38.6 1.0 CG2 A:ILE197 4.9 19.0 1.0 C A:SER198 5.0 20.3 1.0 C A:PRO195 5.0 18.6 1.0 CG A:TYR193 5.0 13.8 1.0 CA A:ASP200 5.0 13.6 1.0 N A:GLY199 5.0 17.9 1.0

Calcium binding site 4 out of 4 in the Thermolysin in Complex with UBTLN31


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin in Complex with UBTLN31 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca329 b:9.2 occ:1.00 O A:GLN61 2.3 8.8 1.0 OD1 A:ASP59 2.4 9.4 1.0 O A:HOH474 2.4 12.1 1.0 OD1 A:ASP57 2.4 9.3 1.0 O A:HOH498 2.4 10.8 1.0 O A:HOH468 2.4 9.6 1.0 OD2 A:ASP57 2.6 9.3 1.0 CG A:ASP57 2.8 9.1 1.0 CG A:ASP59 3.4 10.2 1.0 C A:GLN61 3.4 8.4 1.0 OD2 A:ASP59 3.8 12.4 1.0 N A:GLN61 3.9 8.9 1.0 O A:HOH526 4.0 14.9 1.0 CA A:GLN61 4.1 9.4 0.5 CA A:GLN61 4.1 9.3 0.5 CB A:GLN61 4.3 10.8 0.5 N A:ASP59 4.3 9.6 1.0 CB A:GLN61 4.3 10.7 0.5 CB A:ASP57 4.3 8.3 1.0 O A:HOH482 4.5 12.6 1.0 N A:PHE62 4.5 7.2 1.0 O A:HOH559 4.6 22.4 1.0 CB A:ASP59 4.6 9.7 1.0 N A:ASN60 4.6 9.1 1.0 OD2 A:ASP67 4.6 9.6 1.0 O A:HOH458 4.6 9.3 1.0 CA A:PHE62 4.8 8.0 1.0 N A:ALA58 4.8 8.7 1.0 CA A:ASP59 4.8 8.9 1.0 O A:HOH642 4.8 31.3 1.0 O A:HOH622 4.8 30.4 1.0 C A:ASP59 4.9 8.7 1.0

A.Biela, N.Nasief, A.Heine, D.Hangauer, G.Klebe. Thermolysin Inhibition To Be Published.